Align internal parts of several meshes to the exact same "height", for 3d printing
It's certainly an awkward task, but doable if I understand the situation correctly.
In short I would develop an alignment mechanism with an armature:

Snapping the head and tail of corresponding armature bones to each hole of a bone model.
Parent each bone model to it's respective armature bone.
Duplicate another armature bone per existing armature bone to serve as a target for a damped track bone constraint.
Enable &quot;affect only locations&quot; in the viewport and scale all of your bones in Pose mode to zero in the z-axis.

Here's a brief video of the process.